Advances in agronomy volume 78

Contents CONTRIBUTORS PREFACE ix xi KEEPING IN TOUCH: MICROBIAL LIFE ON SOIL PARTICLE SURFACES Aaron L Mills I Introduction II Nature of Soil Particles Related to Microbial Attachment A Particle-size Distributions B Chemical Distribution III Benefits of Living on Particles A Particle Surfaces as a Physical Substrate for Collection of Nutrients B Utilization of the Particle as a Chemical Substrate IV Importance of Attached Microbes in Soil A Numbers of Attached Versus Free-living Microbes B Phylogeny of Attached Versus Free-living Microbes C Quantitative Considerations of Activity of Attached Versus Non-attached V Diversity of Modes of Attachment A Reversible Versus Non-reversible B Electrostatics C Appendages and Cements VI Effects of Saturated Versus Unsaturated Conditions VII Summary References 4 11 11 14 17 17 18 18 19 19 19 31 33 35 36 THE HISTORY AND SUCCESS OF THE PUBLIC- PRIVATE PROJECT ON GERMPLASM ENHANCEMENT OF MAIZE (GEM) Linda M Pollak I Introduction A The Need for Maize Enhancement B The Latin American Maize Project II GEM’s Development A Public/private US Agricultural Research B Public and Private Interaction to Organize GEM C GEM’s Objective III GEM’s Administration A Organization B Funding Mechanism v 46 46 49 50 50 51 54 55 55 58 vi CONTENTS IV Breeding Activities and Results V Value-added Trait Analyses and Results A The Need for Improving Value-added Traits B The Value-added Trait Research Component of GEM C Grain Composition D Starch Quality E Oil Quality VI Public Cooperator Research and Results A European Corn Borer Resistance B Characterizing LAMP Accessions and Their Crosses for Wet-milling Efficiency C Other Significant Public Cooperator Findings VII Conclusions A Factors Responsible for GEM’s Successful Public/private Collaboration B Extending GEM’s Concept C GEM’s Future References 58 67 67 68 68 70 72 74 75 77 79 80 80 81 83 83 MICROBIOLOGICAL AND BIOCHEMICAL INDEXING SYSTEMS FOR ASSESSING QUALITY OF ACID SOILS Zhenli He, X E Yang, V C Baligar and D V Calvert I Introduction II Acid Soil Distribution in the World III Quality Characteristics of Acidic Soil A Definition and Attributes of Soil Quality B Quality Characteristics of Acidic Soils IV Measurement of Microbiological and Biochemical Parameters in Acidic Soils A Microbial Biomass Carbon, Nitrogen, and Phosphorus B Microbial Turnover of Carbon, Nitrogen, and Phosphorus C Microbial Community Structures D Soil Enzyme Activity V Microbiological and Biochemical Indicators of Acid Soil Quality A Microbial Biomass B Microbial Biomass Turnover C Microbial Biomass-related Indicators D Microbial Community Structure Indicators E Enzyme Activities VI Soil pH Versus Microbiological and Biochemical Indicators VII Development of Acid Soil Quality Indexing Systems VIII Limitations and Prospective Acknowledgments References 90 91 92 92 95 96 97 102 103 104 105 108 115 116 118 119 121 124 128 129 129 CONTENTS vii POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON Jonathan F Wendel and Richard C Cronn I Introduction II Taxonomic, Cytogenetic, and Phylogenetic Framework A Origin and Diversification of the Gossypieae, the Cotton Tribe B Emergence and Diversification of the Genus Gossypium C Chromosomal Evolution and the Origin of the Polyploids D Phylogenetic Relationships and the Temporal Scale of Divergence III Speciation Mechanisms A A Fondness for Trans-oceanic Voyages B A Propensity for Interspecific Gene Exchange IV Origin of the Allopolyploids A Time of Formation B Parentage of the Allopolyploids V Polyploid Evolution A Repeated Cycles of Genome Duplication B Chromosomal Stabilization C Increased Recombination in Polyploid Gossypium D A Diverse Array of Genic and Genomic Interactions E Differential Evolution of Cohabiting Genomes VI Ecological Consequences of Polyploidization VII Polyploidy and Fiber VIII Concluding Remarks References 140 142 142 144 148 150 155 155 155 158 158 161 165 165 168 168 169 173 175 176 178 179 DEVELOPMENT OF ACIDIC SUBSURFACE LAYERS SOIL UNDER VARIOUS MANAGEMENT SYSTEMS Keryn I Paul, A Scott Black and Mark K Conyers OF I Introduction II Widespread Occurrence of Acidic Subsurface Layers III Detrimental Effects of Acidic Subsurface Layers on Agricultural Production A Water and Nutrient Limitations due to Poor Root Growth B Suppression of N Mineralisation C Poor Root Nodulation of Legumes D Poor Growth Response to Topdressing of P Fertiliser E Poor Growth Response to Lime Application IV Rate of Development of Acidic Subsurface Layers V Cause of Development of Acidic Subsurface Layers A Plant N Uptake B Plant Residue Return C Mn Reduction and Oxidation 188 189 189 189 192 192 193 193 193 195 195 197 200 viii VI VII VIII IX CONTENTS D Urine Excretion from Grazing Stock E Soil pH Buffering Capacity Environmental Factors Affecting the Difference in pH Between Surface and Subsurface Layers A Soil Fertility B Initial Soil pH C Rainfall and Fluctuations in Soil Moisture Content D Earthworm Populations Management Factors Affecting the Difference in pH Between Surface and Subsurface Layers A Agricultural Production B Plant Species Grown C Productivity and the Quantity of Plant Residues Added to the Soil Surface D Minimum Soil Disturbance and Tillage E Fertiliser Application F Lime Application Management Implications Conclusions References 200 201 201 201 201 202 203 204 204 205 208 208 209 209 210 211 212 SOIL ACIDIFICATION AND LIMING INTERACTIONS WITH NUTRIENT AND HEAVY METAL TRANSFORMATION AND BIOAVAILABILITY Nanthi S Bolan, Domy C Adriano and Denis Curtin I Introduction II Processes of Acid Generation in Soils A Natural Ecosystems B Managed Ecosystems III Effect of Soil Acidity on Nutrient and Heavy Metal Transformation in Soils A Plant Nutrients B Heavy Metals IV Amelioration of Soil Acidity Through Liming A Liming Materials B Effects of Liming V Lime, Nutrient and Heavy Metal Interactions A Plant Nutrients B Heavy Metals VI Conclusions and Future Research Needs References 216 218 218 223 230 231 234 237 237 239 242 242 256 258 260 INDEX 273 KEEPING IN TOUCH: MICROBIAL LIFE ON SOIL PARTICLE SURFACES Aaron L Mills Laboratory of Microbial Ecology, Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia 22904-4123, USA I Introduction II Nature of Soil Particles Related to Microbial Attachment A Particle-size Distributions B Chemical Distribution III Benefits of Living on Particles A Particle Surfaces as a Physical Substrate for Collection of Nutrients B Utilization of the Particle as a Chemical Substrate IV Importance of Attached Microbes in Soil A Numbers of Attached Versus Free-living Microbes B Phylogeny of Attached Versus Free-living Microbes C Quantitative Considerations of Activity of Attached Versus Non-attached V Diversity of Modes of Attachment A Reversible Versus Non-reversible B Electrostatics C Appendages and Cements VI Effects of Saturated Versus Unsaturated Conditions VII Summary References Microorganisms in unsaturated soil live in a world dominated by the presence of extensive surfaces, both solid and gas –liquid interfacial surfaces Particle attachment in soils is similar to particle attachment in aquatic systems, which, because of the high abundance of suspended populations has been widely studied Although there seems to be a general advantage to the microbes living at the interfaces in terms of enhanced nutrient concentrations and the potential to use many of the physical substrata themselves as energy or nutrient sources, the thickness of the water films in unsaturated conditions leaves the microbes little option except to adhere to the surfaces Initial attachment to the surfaces appears to be dominated by electrostatic and hydrophobic effects that are described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory for negatively charged cells and particles These effects result in reversible attachment and the cells are subject to rapid detachment with slight changes in solution chemistry and removal by hydraulic shear Coatings play an important role in attachment, with metal oxide coatings Advances in Agronomy, Volume 78 Copyright q 2003 by Academic Press All rights of reproduction in any form reserved 0065-2113/02$35.00 A L MILLS conferring a positive charge to the particle surface resulting in a much tighter adhesion of the microbial cells to the surface Attachment of the organisms to the particles by direct surface contact through appendages such as fimbriae or deposition of polysaccharidic slime results in irreversible attachment that can lead to buildup of colonies and biofilms In this chapter, considerations of theory are presented as they pertain to soil organisms, and abundant use of examples from aquatic habitats exemplifies principles and ideas not easily studied in unsaturated soil The importance of attachment to the gas – liquid interface is also highlighted q 2003 Academic Press I INTRODUCTION The soil habitat represents a unique but extensive environment in which microorganisms live and carry out biogeochemical reactions critical to the maintenance of ecosystems The uniqueness of the soil is related to the vast amount of particle surface area contained there Other habitats also contain particles, often with a large surface area, but soils are dominated by surfaces and the matrix is generally hydrologically unsaturated The combination of particle surface area with thin water films makes soils different in many respects from their saturated counterparts in aquatic sediments and aquifers formed from unconsolidated materials The purpose of this chapter is to examine the relationship of soil microorganisms to soil particles in terms of their tendency to attach themselves to the particles Much of the chapter will examine mechanisms of attachment, but this information is best understood in the context of why the bacteria attach to the particles To accomplish this goal, it will be necessary to consider particle attachment in general, including information from other habitats such as in lakes and marine environments Thus, while the focus of this discussion is attachment in soils, principles will be derived from other environments as needed and justified Fletcher recently published an excellent volume (Fletcher, 1996) that examined in general the attachment of microbes to surfaces from both an ecological and physiological viewpoint Part of this chapter formed part of a contribution to this volume, and the book also served as an important starting point for a number of topics covered here Readers are encouraged to use the chapters contained in this reference for a more detailed coverage of the general topic of microorganisms and surfaces than can be accomplished here Attachment to particles could arise due to three possible reasons Attachment might occur completely as a result of serendipity Bacterial attachment might confer neither an advantage nor a disadvantage to the organisms, and there might be no active mechanism that pulls bacteria to the surface of particles Experience teaches us that while events frequently arise spontaneously, their persistence in biological systems generally arises from some selective advantage conferred on the organisms involved Furthermore, the degree to which bacteria attach to MICROBES AND SOIL PARTICLE SURFACES particles in soils and in aquatic ecosystems and the strength of the association once established, argue strongly against happenstance as the causative agent for bacterial attachment A second possible reason for the high frequency of particle association by bacteria is that there is a selective advantage to the organisms to live in close association with a particle surface In biological systems, behaviors that are not advantageous to the populations are generally lost over evolutionary time It is possible that attachment represents a neutral behavior (a rationale for which is discussed in the following paragraph), but we can certainly be sure that particle attachment does not represent a behavior that is generally detrimental to the cells If this were the case, the attached bacteria would quickly be eliminated by competition with the suspended bacteria for limiting resources Indeed, it is likely that attachment represents an advantage to the organisms in some major way; they may obtain some essential element from the particle grains, they might obtain energy from organic or inorganic molecules tightly sorbed to the mineral grain surface, or they might benefit from living in a chemically richer aqueous environment due to enhanced concentrations of soluble nutrients in the proximity of the grain surface In some cases, attachment to particles might provide partial or complete protection from grazing by bacterivorous organisms All these possibilities will be discussed in detail later A third possible reason for particle attachment in soils also exists In unsaturated soils, microbes have little choice but to exist at or near the surface of the soil particles Although filamentous fungi and actinomycetes have been observed to span unsaturated voids, single-celled organisms are limited to total immersion to be active (Metting, 1993); furthermore, nutritional uptake requires an aqueous phase for all phenotypes (Harris, 1981) Even under the so-called optimal soil moisture conditions in which the pore space of a silt loam soil is approximately 50% filled with water, the amount of water associated with each particle does not leave much room for the microbes to move a great distance from the surface of a particle A simple calculation illustrates this point Consider a soil composed entirely of uniformly spherical particles that are in the mid-silt-size range, i.e., 0.025 cm in diameter Consider further that the soil has a bulk density of 1.2 g cm23 A final assumption is that all the water is perfectly uniformly distributed on the entire surface of all particles (note that the particles not actually touch under this assumption) Under these oversimplified assumptions, each particle is coated with a film of water that is only about 6.4 mm thick While no such soil exists in reality, and the actual thickness of water films under realistic soil conditions varies from a few molecules to millimeters, there is not much volume in the soil that permits the microbes to be very far from the surface of a mineral or organic soil particle Indeed, Mills and Powelson (1996) estimated from literature data (Gardner, 1956; Green et al., 1964; Holmes et al., 1960; Kemper and Rollins, 1966) that at field capacity (soil moisture tension of 0.33 bar), one might expect a film thickness of only 0.2 –0.3 mm assuming A L MILLS uniform coverage of the grains by the water film Metting (1993) calculated that at a soil matric potential of 0.01 MPa, capillaries less than 30 mm in diameter would be saturated, but at 0.03 MPa, saturation would be only in pores of less than mm diameter When the potential is less than 0.5 MPa there is only a film of water a few molecules thick The principal point is that the water film thins quickly as the degree of saturation decreases, forcing the microbial cells even closer to the grain surface The argument presented in the preceding paragraph might be quite compelling as a complete explanation if it were not for the fact that soils are not the only place where particle association is observed In soils, attachment is so heavily dominant because the soil habitat is completely dominated by particle surface area surrounded by the thin films of water In all systems the degree of particle association appears to be correlated to both the number of bacterial cells and the number of particles present We cannot conclude that either selective advantage or necessity is the single reason for attachment as the way of life in soils Obviously, the answer is a combination of the two factors The fact that water films are generally thin and vegetative bacteria are forced to live, therefore, close to the particle surfaces is obvious The ensuing discussion, therefore, will concentrate on factors that confer advantage to the organisms living on particle surfaces in soil II NATURE OF SOIL PARTICLES RELATED TO MICROBIAL ATTACHMENT A PARTICLE-SIZE DISTRIBUTIONS A number of factors influence the attachment and permanent association of bacteria with soil particles In addition to particle composition (discussed later), particle size seems to play an important role in determining the distribution of microbial populations in soil aggregates A study by Hattori (1973) showed the strong quantitative relationship between clay particles and bacterial cells (Fig 1) A number of studies have shown that both the cell number and the bacterial biomass tend to be most concentrated in the smaller size silt and clay fractions (Jocteur Monrozier et al., 1991; Kandeler et al., 2000, 2001; vanGestel et al., 1996) Obviously, therefore, the bacteria are mainly present in micropores of 5– 30 mm (Amato and Ladd, 1992; Hassink et al., 1993; Kirchmann and Gerzabek, 1999) Analysis of the distribution of microbial enzyme activities suggest that the bacterial activities are dominant in the silt and clay fractions, whereas enzyme activities that indicate fungi are highest in the sand fraction (Gerzabek et al., 2002; Kandeler et al., 1999, 2000; Stemmer et al., 1998, 1999) There may be, however, even more qualitative selection for particle sizes than at a cell domain MICROBES AND SOIL PARTICLE SURFACES Figure Adhesion of cells of E coli to particles of sodium pyrophyllite as a function of particle concentration Both cells and clay had effective mean diameters of 0.8 and 0.9 mm, respectively Figure redrawn from Marshall (1980); original data from Hattori (1973) Reproduced with permission of John Wiley & Sons level, i.e., bacteria versus fungi A recent article by Sessitsch et al (2001) reported that not only were the numbers of attached bacterial cells greater in the finer textured fraction of Dutch soils, but also the community composition differed Termmal Restriction Fragment Length Polymorphism (T-RFLP) analysis of the communities associated with the different size fraction indicated that different organisms were the dominant inhabitants of the coarser particles as compared with the fine materials These authors also suggested that diversity of the amplifiable genotypes in the clay fractions was greater than that in the coarser A L MILLS fractions based on the number of fragments recovered in T-RFLP analysis of the particle associated DNA in each size fraction Much of the difference noted was attributed to organic amendments in the several soils examined, and to possible competition with fungi in the coarser particle sizes There is good reason why clay fractions would have the maximum interactions with bacteria The particles’ small size yields an enormous surface area per unit weight of solid, and the crystal structure of clays tends to engender a strong net negative charge on the surface that can attract nutrients, organics, and under the right circumstances, the bacterial cells themselves Quartz and feldspars, materials with relatively inert chemical behavior usually dominate sand-size grains As particles weather to smaller silt and clay-size particles, their composition changes to layer silicates; the smaller soil particles present not only a larger total surface area, but also a more reactive one as well The influence of the finer textured materials is, therefore, a combination of the surface area increase and the specific mineralogy of the particles Table I shows how cation exchange capacity (CEC) increases with increasing fineness of texture The range of values for exchange capacity for each textural category reflects different mineralogy and different amounts of organic matter present in individual soils Most soil particles not present surfaces with the reactivity reflecting only the base mineralogy of the particle Many particles have some portion of their surface coated with reactive materials, such as iron, aluminum, and manganese oxides and hydroxides, and organic matter These coatings can alter the reactive surfaces of the particles, in some cases changing the negative surface charge to neutral or positive, and they can otherwise add reactivity to only slightly reactive surfaces In this way, even quartz sand can become highly reactive by adsorption of a coat of negative metal oxide or organic matter The issue of coating and soil particles’ tendency to sorb bacteria will be discussed later Table I Change in CEC with Change in Soil Texture Exchange capacity (Cmol g21) Textural classification Sand Sandy loam Loam Silt loam Clay and clay loam No of soils Average Range 2.8 ^ 1.1 6.8 ^ 5.8 12.2 ^ 3.6 17.8 ^ 5.6 25.3 ^ 20.3 2.0– 3.5 2.3– 17.1 7.5– 15.9 9.4– 26.3 4.0– 57.5 Note Data for averages are expressed as the mean and standard deviation for the soils, and the range represents the minimum and maximum values reported within the textural category Source Mills and Powelson (1996) based on data taken from Brady (1984) Reproduced with permission of Wiley–Liss SOIL ACIDIFICATION AND LIMING INTERACTIONS 265 Frazer, L (2001) Probing the depths of a solution for acid mine drainage Environ Health Perspect 109, 486–489 Friesen, D K., Miller, M H., and Juo, A S R (1980) Liming and lime –phosphorus–zinc interactions in two Nigerian Ultisols I Interactions in the soil Soil Sci Soc Am J 44, 1221–1226 Friesen, D K., Miller, M H., and Juo, A S R (1980) Liming and lime –phosphorus–zinc interactions in two Nigerian Ultisols II Effects on maize root and shoot growth Soil Sci Soc Am J 44, 1227–1232 Galindo, G.G., and Bingham, F T (1977) Homovalent and heterovalent cation exchange equilibria in soils with variable surface charge Soil Sci Soc Am Proc 41, 883– 886 Gardner, E H., Derics, I A., and Basaraba, J (1965) Mineralization of nitrogen in some Fraser valley soils as affected by liming Can J Soil Sci 45, 355– 360 Godo, G H., and Reisenauer, H M (1980) Plant effects on soil manganese availability Soil Sci Soc Am J 44, 993–995 Goedert, W J., Corey, R B., and Syers, J K (1975) Lime effects on potassium equilibria in soils of Rio Grande Do Sul, Brazil Soil Sci 120, 107– 111 Gray, C W., McLaren, R G., Roberts, A H C., and Condron, L M (1999) Effect of soil pH on cadmium phytoavailability in some New Zealand soils NZ J Crop Hort 27, 169–179 Gregan, P D., Hirth, J R., and Conyers, M K (1989) Amelioration of soil acidity by liming and other amendments In “Soil Acidity and Plant Growth” (A D Robson, Ed.), pp 205–264 Academic Press, New York Grego, S., Moscatelli, M C., Marinari, S., and Badalucco, L (2000) The influence of liming and natural acidification on chemical and biological processes of an Italian forest soil Agrochimica 44, 161–170 Grove, J H., Sumner, M E., and Syers, J K (1981) Effect of lime on exchangeable magnesium in variable charge soils Soil Sci Soc Am J 45, 497–500 Gupta, U C (1972) Effects of 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Effect of parent material, natural available soil boron, and applied boron and lime on the growth and chemical composition of lucerne on some acidic soils of the Central Tablelands of New South Wales Aust J Expt Agric Ani Husb 22, 317 –323 Han, D H., and Lee, J H (1996) Effects of liming on uptake of lead and cadmium by Raphanus sativa Arch Environ Cont Toxicol 31, 488 –493 Harter, R D (1991) Micronutrient adsorption– desorption reactions in soils SSSA In “Micronutrients in Agriculture” (J J Mortvedt,, F R Cox,, L M Shuman, and R M Welch, Eds.), (2nd ed.) 4, pp 59–88 Soil Sci Soc Am, Madison, WI Haynes, R J (1983) Soil acidification induced by leguminous crops Grass Forage Sci 38, 1–11 Haynes, R J (1984) Lime and phosphate in the soil–plant system Adv Agron 37, 249– 467 266 N S BOLAN, D C ADRIANO AND D CURTIN Haynes, R J (1990) Active ion uptake and maintenance of cation–anion balance: A critical examination of their role in regulating rhizosphere pH Plant Soil 126, 247– 264 Haynes, R 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(1982) Table beet yield and boron deficiency as influenced by lime, nitrogen and boron Soil Sci Soc Am J 46, 1190–1192 Hesterberg, D., Bril, J., and Delcastilho, P (1993) Thermodynamic modeling of zinc, cadmium, and copper solubilities in a manured, acidic loamy-sand topsoil J Environ Qual 22, 681 –688 Hingston, F J (1981) A review of anion adsorption In “Adsorption of Inorganics at Solid– Liquid Interfaces” (M A Anderson, and A J Robin, Eds.), pp 51 –90 Ann Arbor Science, Ann Arbor, MI Hochman, Z., Edmeades, D C., and White, E (1992) Changes in effective CEC and exchangeable aluminium with soil pH in lime-amended soil Aust J Soil Res 30, 177 –187 Hodgson, J F., Lindsay, W L., and Trierwei, J F (1966) Micronutrient cation complexing in soil solution Complexing of zinc and copper in displaced solution from calcareous soils Soil Sci Soc Am J 30, 723–726 Holford, I C R., Schweitzer, B E., and Crocker, G J (1994) Long-term effects of lime on soil phosphorus solubility and sorption in eight 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and pig manure as ameliorants for revegetating lead/zinc mine tailings: A greenhouse study Biores Technol 69, 35–43 Zimdahl, R L., and Foster, I M (1976) Influence of applied phosphorus, manure, or lime on uptake of lead from soil J Environ Qual 5, 31 –34 Index A acid drainage, 220– acid precipitation, 221–3 acid soils, 89 –138 see also acid subsurface layers; liming; soil acidification characteristics and properties, 92 –6 distribution, 91– enzyme activity, 104–5, 119 –21 fertility and chemical properties, 93–4, 108 –12 microbial biomass estimation, 97 –102 microbial biomass turnover, 115–16 microbial community structure, 103–4, 118 –19 nutrient turnover, 102– occurrence, 90 pH value, 121– quality indexing systems, 124–8 quality indicators, 105 –21 acidic subsurface layers, 187–214 see also soil acidification; soil pH causes, 195 –201 detrimental effects, 189–93 development rate, 193–5 environmental factors, 201–4 management factors and implications, 204 –12 occurrence, 189 poor growth, 189 –92, 193 surface mixing, 211 agricultural production on acid soils, 204 –5, 208 Alfisols, 92 allopolyploid cotton, 141–2, 149 –50 formation and diversification, 158–61 parentage, 161 –5 phylogeny, 151–2, 167, 171 polyphyly, 164 aluminium, 247, 249 amelioration of acid soils, 237–42 animal feed, 46, 68–70 anion exclusion, 24 arsenic, 236, 248, 257–8 attached microbes, see microbial attachment B bacteria see also microbial attachment ammonium oxidation, 13 chemical substrate, 14 –17 electrostatics, 19–31 hydrophobic effects, 19–26, 30 microfibrillar structures, 31–2 physical substrate, 11 –13 basal respiration rate, 117 BATH (bacterial adherence to hydrocarbons) method, 24–5 biochemical soil quality indicators, 105 –21 biodegradation, 12 BIOLOG method, 104 biological amelioration, 241–2 biological properties of soils, 92 –4 biomass, see microbial biomass breeding of corn, 47– 8, 49–50 evaluation of crosses, 61–6 GEM activities and results, 58–67 GEM project, 51–4 GEM protocol, 59–60 C cadmium, 234 –6, 247, 257 calcium, 233, 244, 253– carbon, microbial, 97 –103, 108 –9, 111–12, 114–15 carbon cycle, 219, 223 –4 cation exchange capacity, (CEC), 6, 9–10 CFE, see chloroform fumigation–extraction CFI, see chloroform fumigation–incubation charge of organic particles, –10, 17 see also electrostatics chemical amelioration, 240–1 chemical distribution of microbes, 7–11 chemical properties of soils, 92, 93 China, red soils, 110 chloroform fumigation–extraction (CFE), 97–101 chloroform fumigation–incubation (CFI), 97, 98, 100 chromatography, 24–5 chromium, 236, 248, 258 273 274 INDEX chromosomes see also genomes evolution (Gossypium), 148–50 stabilization, 168 clay fractions, 5–6 clover, 199, 200 see also legumes coatings, 6, 10–11 mineral, 27–9 organic, 29 –31 collaboration GEM project, 51–8 LAMP project, 46, 48, 49–50, 51, 81– contamination of soils, 112 copper, 233, 245, 256 corn see also germplasm enhancement of maize breeding activities and results, 47–8, 49–50, 58–67 enhancement need, 46–9 European corn borer resistance, 75–7 genetic vulnerability, 46–7 germplasm, 47 –9 grain composition, 68–72 oil quality, 72–4, 75 starch quality, 70–2, 73 –4, 78 corn oil, 72 –4, 75 corn starch, 70– 2, 73–4, 78 cotton, 139 –86 see also allopolyploid cotton; diploid cotton; Gossypium; poplyploid cotton cultivation, 140 –1 fibers, 139, 140, 176 –8 origin of tribe, 142–4 Cretaceous, Gossypium origin, 153–4, 158–9 crops see also corn; legumes; maize; wheat soil depth and pH, 190– 1, 194, 197, 200 subsurface acidification, 204 –5, 208 cultivation of cotton, 140–1 cytoplasmic capture, Gossypium, 156– 7, 164 D Derjaguin– Landau–Verwey–Overbeck (DLVO) theory, 22 differential scanning calorimetry (DSC), corn, 71–2, 73–4 diploid cotton, 141 –2, 147–8, 151–2, 161–2, 166–9, 171 dispersal of cotton, 144–8, 155 DLVO theory, see Derjaguin–Landau– Verwey–Overbeck theory DNA sequence data, Gossypium, 150 –4, 159– 60 drainage, acid, 220–1 DSC, see differential scanning calorimetry duplication genes, 169 –73 genomes, 165–7 E E coli cells adhesion, earthworms, 96, 203– 4, 211 ecological consequences of polyploidization, 175– ecosystems managed, 223–9 natural, 218–23 electrostatics, 19–31 DLVO theory, 22 hydrophobic effects, 19 –26 mineral coatings, 27 –9 organic coatings, 29–31 potential, 22 primary mineral differences, 26–7 repulsion, 24 energy content of corn, 68–9 environmental factors, soil acidification, 201–4 enzyme activity, acid soils, 104–5, 119–21 European corn borer resistance, 75–7 evolutionary history of cotton, 139–86 allopolyploids, 158 –65, 171 diploids, 171 polyploids, 165 –75 exotic germplasm, 54 –5 F farming activities, 223–9 fauna, 96, 203–4, 211 see also bacteria fertility, see soil fertility fertilizers, 209, 226–9, 259 see also liming; soil pH fibers, cotton, 139, 140, 176–8 fimbriae, 31 foodstuff, 46, 68–70 free-living microbes, 17–19 fumigation techniques, 97– 101 funding, GEM project, 58 INDEX G gas–water interface (GWI), 33 –5 GEM, see germplasm enhancement of maize gene interactions, Gossypium, 155 –8, 169– 73 genealogy, Gossypium, 150–3 genetic base of corn, 46– genomes (cotton), 141–2 composition, 149–50 doubling cycles, 165 –7 evolution, 151 –3, 173 –5 interactions, 169–73 parentage, 161 –5 size variation, 148–9 genotypes, 210 germplasm enhancement of maize (GEM), 45 –87 bank accessions, 48 breeding activities and results, 58–67 concept expansion, 81–3 European corn borer resistance, 75– funding mechanism, 58 grain composition, 68– 72 international collaboration, 49–50 need for, 46 –9 objective, 54–5 organization, 55–8 public cooperator findings, 79–80 public and private interaction, 51–4 research projects, 52– 3, 56–7 success factors, 80– value-added trait analysis, 67 –8 wet milling efficiency, 77– Gossypieae tribe, 142–4 Gossypium, 139– 86 alloploid origin, 158–65 characters, 143 chromosomal evolution, 148–50 chromosome stabilization, 168 diploids, 147–8, 151 –2, 161 –2, 166–9, 171 divergence events, 153–4, 158–61 emergence and diversification, 144– 8, 155 G barbadense, 140– 2, 150, 152, 161–2, 164 –5, 172 G gossipioides, 164 –5 G hirsutum, 140–2, 150, 152, 172 G raimondii, 161 –2, 164– genealogy, 150– genic and genomic interactions, 155 –8, 169 –73 genome composition, 149 –50 275 genome doubling, 165– genome evolution, 151 –3, 173–5 genome size variation, 148–9 hybridization, 155–8 phylogeny, 150–4 polyploid evolution, 165–75 recombination, 168 –9 grain see also corn; maize; wheat composition, 68– 72 legumes, 206 moisture values, 62–5 grazing stock, urine excretion, 200–1 growth, 189 –92, 193, 217 see also agricultural production; breeding of corn; crops GWI, see gas– water interface H heavy metals contamination, 112 liming effects, 247 –8, 256– 8, 259 soil acidification, 234–6 HIC, see hydrophobic interaction chromatography humus see also organic matter hybridization, Gossypium, 155– hydrophobic effects, 19–26, 30 hydrophobic interaction chromatography (HIC), 24–5 I immersion of microbes, indexing systems, see acid soils indicators of soil quality, 105–21 contamination, 112 –15 fertility, 108–12 microbial biomass-related, 116 –21 microbial community structure, 118–19 pH value, 121 –4 industrial activities, 218–23 international collaboration, 46, 49–50, 51, 81–2 iron, 234, 246, 256 L Latin American Maize Project (LAMP), 46, 48, 49–50, 81 –2 276 INDEX lead, 248, 258 legumes poor root nodulation, 192–3 subsurface acidification, 196 –7, 199, 200, 205–7 liming, 122 –3, 259 amelioration of acid soils, 239 –42 heavy metal interactions, 247–8, 256 –8 materials, 237 –9 nutrient interactions, 242–56 poor growth response, 193 soil pH, 209 –10, 211 uses, 217 –18 M magnesium, 233, 244, 253–5 maize enhancement, 45– 87 see also germplasm enhancement of maize breeders, 51 –4 germplasm, 47 –9 grain composition, 68–72 LAMP project, 46, 48, 49–50, 51, 81– need for, 46–9 managed ecosystems, 223 –9 manganese, 200, 233–4, 247, 258 mercury, 248 metal oxide coatings, 28–9 metals, 243, 244–6 see also heavy metals; trace elements microbial attachment, 1–43 appendages and cements, 31–2 chemical distribution, –11 chemical substrate, 14–17 electrostatics, 19 –31 importance, 17–19 particle-size distribution, 4–7 physical substrate, 11–13 reasons, 2–3 saturated v unsaturated conditions, 33–5 microbial biomass estimation, 97 –102 microbial metabolic quotient, 117–18 microbial quotient, 116 –17 nutrient turnover, 102–3 related indicators, 116 –21 soil contamination indicator, 112–15 soil fertility indicator, 108–12 turnover, 115 –16 microbial community structure, 103 –4, 118–19 microfibrillar structures, 31 –2 mineral coatings, 27 –9 mineral particles chemical substrate, 14–15 distribution, 7–8 microbial attachment, 26– organic-coated, 10 –11 moisture, see rainfall; water molybdenum, 246, 256 N natural ecosystems, 218–23 nickel, 248, 258 nitrification, 202 nitrifying bacteria, 13 nitrogen, 219 fertilizers, 227–8 liming effects, 242–3 microbial, 101, 102 –3, 108– 9, 111–12, 114– 16 mineralisation suppression, 192 plant uptake and soil pH, 195 –7 soil acidity effects, 231 transformation, 225–6 uptake and assimilation, 224–5 non-reversible attachment, 19 nutrients, 10 acidic layers, 189–92 enhancement, 11–13 fertilizers, 227 liming interactions, 242–56 microbial biomass estimation, 97– 102 microbial biomass fertility, 108–12 microbial turnover, 102– soil acidification, 230 –4 O oil quality, corn, 72–4, 75 organic coatings, 29–31 organic matter see also plant residues acid soils, 96 charge, 7, 9–10 composition and properties, 8–10 decomposition, 225 humus, microbial attachment, 15– 17 timing effects, 254 organic-coated mineral particles, 10–11 organisms, see bacteria; fauna INDEX Oxisols, 92, 95 see also acid soils P particle attachment, see microbial attachment; mineral particles; organic matter particle-size distribution, 4–7 pasture, 190, 205 –8 pH, see soil pH phosphate fertilizers, 228, 259 phosphate rocks (PRs), 237–9 phosphorus fertilizer, 193 liming effects, 238, 243, 249–51 microbial, 101– 3, 111–12, 114–16 P-sparing effect, 250 soil acidity effects, 231 –2 phylogeny allopolyploids, 158 –65, 171 diploids, 171 Gossypium, 143–4, 150–4 microbes, 18 polyphyly, 164 physical amelioration of soil, 240 plants acification processes, 223 –5 growth, 189– 92, 193, 217 nitrogen uptake, 195– nutrients, 231–4, 242–56 residues, 197–200, 202, 208 species on acid soils, 205–8, 210 Pleistocene, 159– 60 polyphyly, 164 polyploid cotton, 139–86, 141 ecological consequences, 175 –6 evolution, 165 –75 fiber, 176–8 genomic composition, 149–50 recombination, 168 –9 taxonomic diversity, 150 potassium, 232, 243, 251 precipitation, 202–3, 221 –3 primary nutrients, 231–2, 242 –51 private sector, see public/private cooperation protein, corn, 68–9 protocol, corn breeding, 59–60 proton generation, 219–20 PRs, see phosphate rocks public/private cooperation GEM project, 51 –8 277 GEM research and results, 74–80 GEM success factors, 80–2 US agricultural research, 50– pyrite, 14–15, 219–21, 258 –9 Q quality, see soil quality R rainfall, acid, 202–3, 221–3 red soils, 110– 11 research GEM projects, 52–3, 56 –7, 74–80 US agriculture, 50–1 value-added trait, 68 residues, see plant residues reversible attachment, 19 roots, 189–93 S saturation, 33– secondary nutrients, 232–3, 242–3, 252–8 selenium, 236, 245, 258 silicates, –8 size distribution, soil particles, 4–7 soil acidification, 215–72 see also acid soils; acidic subsurface layers; liming acid drainage, 220 –1 acid precipitation, 219, 221 –3 amelioration through liming, 237–42 causes and effects, 216–18 fertilizer use, 226 –9 heavy metal transformation, 234 –6 lime, nutrient and heavy metal interactions, 242–58 pasture, 190, 205–8 plant-induced processes, 223–5 primary nutrients, 230–2, 242–51 secondary nutrients, 232–3, 242–3, 252 –8 soil-induced processes, 225–6 trace elements, 233–4, 245 –6 soil disturbance, 208 soil enzyme activity, 104– 5, 119–21 soil fertility, 201 acid soils, 93 –4 indicators, 108–12 liming effects, 238 –42 278 INDEX soil moisture, see soil water soil particles see also mineral particles; organic matter microbial attachment, 1–43 size distribution, 4–7 soil pH, 188 –9 see also acid soils; soil acidification acid soils, 121–4 buffering capacity, 201 changes due to fertilizers, 229 environmental factors, 201 –4 initial value, 201–2 liming effects, 209 –10, 211 management factors, 204–10 nutrient transformation, 230 plant N uptake, 195–7 plant residue returns, 197 –200 variation with depth, 190–2, 194, 197, 200, 204 soil quality, 89–138 see also soil fertility characteristics, 92 –6 contamination indicators, 112 –15 definition, 92 indexing systems, 124–8 microbial biomass indicators, 116–21 minimum data sets, 128 pH indicator, 121 –4 soil water, 3–4, 33–5, 202 –3 soil-induced acidification, 225 –6 speciation mechanisms, Gossypium, 155–8 starch quality (corn), 70– 2, 73–4, 78 substrate induced respiration (SIR), 97, 98, 100–1 subsurface layers, acidic, 187 –214 sulfate fertilizers, 228 –9 sulfides, 220 –1 sulfur, 220 liming effects, 243 –4, 252 –3 soil acidity effects, 232 transformation, 226 uptake and assimilation, 225 sulfur dioxide emissions, 222 T taxonomy, Gossypium, 145 –8, 150 tea bushes, 123– tillage techniques, 208 toxic heavy metals, see heavy metals trace elements, 233 –4, 245– 6, 255–6 U Ultisols, 92, 95 see also acid soils urine excretion by stock, 200 –1 US agriculture, 46 –7, 50–1 V value-added trait analysis, 67 –8 van der Waals minimum, 22 W water, 189 –92 see also soil water wet milling efficiency (corn), 77 –9 wheat, 199 Y yields (corn), 47, 62 –5 Z zeta potential, 21 zinc, 233, 245, 256 ERRATUM Advances in Agronomy, Volume 75 In the References section, page 231, of the chapter “Quantitative Remote Sensing of Soil Properties” by E Ben-Dor, the reference to the article by J A M Dematteˆ and G J Garcia was printed incorrectly The correct version is shown below: Dematteˆ, J A M., and Garcia, G J (1999) Alteration of soil properties through a weathering sequence as evaluated by spectral reflectance Soil Sci Soc Am J 63, 327– 342 The original (incorrect) citation was given as: Alexander, J., Dematte, M., and Garcia, G J (1999) Alteration of soil properties through a weathering sequence as evaluated by spectral reflectance Soil Sci Soc Am J 63, 327 –342 ... completely explain the rapid growth of suspended organisms in sampling containers Kaper et al (1 978) observed a doubling of the number of suspended cells in polyethylene sampling bags within 20 of sample... with metal oxide coatings Advances in Agronomy, Volume 78 Copyright q 2003 by Academic Press All rights of reproduction in any form reserved 0065-2113/02$35.00 A L MILLS conferring a positive charge... are defined by the structural organization of the particles into aggregates (Marshall, 1980) B CHEMICAL DISTRIBUTION MINERAL The most common minerals found in soils are listed in Table II In general,